Identification of rice transcription factors associated with drought tolerance using the Ecotilling method.

Yu S, Liao F, Wang F, Wen W, Li J, Mei H, Luo L - PLoS ONE (2012)

Bottom Line:
The results showed that three genes were associated with the DT index and that five genes were associated with the DT level.The sequences of these associated genes are complex and variable, especially at approximately 1000 bp upstream of the transcription initiation sites.The study illuminated that association analysis aimed at Ecotilling diversity of natural groups could facilitate the isolation of rice genes related to complex quantitative traits.

ABSTRACTThe drought tolerance (DT) of plants is a complex quantitative trait. Under natural and artificial selection, drought tolerance represents the crop survival ability and production capacity under drought conditions (Luo, 2010). To understand the regulation mechanism of varied drought tolerance among rice genotypes, 95 diverse rice landraces or varieties were evaluated within a field screen facility based on the 'line-source soil moisture gradient', and their resistance varied from extremely resistant to sensitive. The method of Ecotype Targeting Induced Local Lesions in Genomes (Ecotilling) was used to analyze the diversity in the promoters of 24 transcription factor families. The bands separated by electrophoresis using Ecotilling were converted into molecular markers. STRUCTURE analysis revealed a value of K = 2, namely, the population with two subgroups (i.e., indica and japonica), which coincided very well with the UPGMA clusters (NTSYS-pc software) using distance-based analysis and InDel markers. Then the association analysis between the promoter diversity of these transcription factors and the DT index/level of each variety was performed. The results showed that three genes were associated with the DT index and that five genes were associated with the DT level. The sequences of these associated genes are complex and variable, especially at approximately 1000 bp upstream of the transcription initiation sites. The study illuminated that association analysis aimed at Ecotilling diversity of natural groups could facilitate the isolation of rice genes related to complex quantitative traits.

pone-0030765-g001: Posterior probabilities (Ln P(D)) from six parallel calculations for each hypothetic number of subpopulations (K) in the range of K = 1 to K = 10.

Mentions:
The model-based method was performed using the TILLING polymorphic loci to recognize the genetic structure of all the 95 samples based on the gene markers distributed in the whole genome. Independent calculations were performed six times for each k value from k = 1 to k = 10. The posterior probability (ln P(D)) sharply increased from k = 1 to k = 2 but slowly after k = 2 (Figure 1). The results of six parallel calculations converged with each other only for k = 1, 2, and 3. However, the clustering structures among rice accessions varied among the parallel calculations for k = 3 and k = 4. The population structure with two subpopulations (i.e., k = 2) was chosen for the samples in this study. The result was similar to the analysis of the mini-core collection of Chinese germplasms [31].

pone-0030765-g001: Posterior probabilities (Ln P(D)) from six parallel calculations for each hypothetic number of subpopulations (K) in the range of K = 1 to K = 10.

Mentions:
The model-based method was performed using the TILLING polymorphic loci to recognize the genetic structure of all the 95 samples based on the gene markers distributed in the whole genome. Independent calculations were performed six times for each k value from k = 1 to k = 10. The posterior probability (ln P(D)) sharply increased from k = 1 to k = 2 but slowly after k = 2 (Figure 1). The results of six parallel calculations converged with each other only for k = 1, 2, and 3. However, the clustering structures among rice accessions varied among the parallel calculations for k = 3 and k = 4. The population structure with two subpopulations (i.e., k = 2) was chosen for the samples in this study. The result was similar to the analysis of the mini-core collection of Chinese germplasms [31].

Bottom Line:
The results showed that three genes were associated with the DT index and that five genes were associated with the DT level.The sequences of these associated genes are complex and variable, especially at approximately 1000 bp upstream of the transcription initiation sites.The study illuminated that association analysis aimed at Ecotilling diversity of natural groups could facilitate the isolation of rice genes related to complex quantitative traits.

ABSTRACTThe drought tolerance (DT) of plants is a complex quantitative trait. Under natural and artificial selection, drought tolerance represents the crop survival ability and production capacity under drought conditions (Luo, 2010). To understand the regulation mechanism of varied drought tolerance among rice genotypes, 95 diverse rice landraces or varieties were evaluated within a field screen facility based on the 'line-source soil moisture gradient', and their resistance varied from extremely resistant to sensitive. The method of Ecotype Targeting Induced Local Lesions in Genomes (Ecotilling) was used to analyze the diversity in the promoters of 24 transcription factor families. The bands separated by electrophoresis using Ecotilling were converted into molecular markers. STRUCTURE analysis revealed a value of K = 2, namely, the population with two subgroups (i.e., indica and japonica), which coincided very well with the UPGMA clusters (NTSYS-pc software) using distance-based analysis and InDel markers. Then the association analysis between the promoter diversity of these transcription factors and the DT index/level of each variety was performed. The results showed that three genes were associated with the DT index and that five genes were associated with the DT level. The sequences of these associated genes are complex and variable, especially at approximately 1000 bp upstream of the transcription initiation sites. The study illuminated that association analysis aimed at Ecotilling diversity of natural groups could facilitate the isolation of rice genes related to complex quantitative traits.